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biopet.biopet
Commits
70865194
Commit
70865194
authored
Oct 21, 2014
by
Peter van 't Hof
Browse files
Fix queue wrapper
parent
08eb14a4
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
70865194
...
...
@@ -40,11 +40,11 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
override
def
commandLine
=
super
.
commandLine
+
required
(
"-I"
,
inputVcf
)
+
required
(
"-o"
,
outputVcf
)
+
optional
(
"-minSampleDepth"
,
minSampleDepth
)
+
optional
(
"-minTotalDepth"
,
minTotalDepth
)
+
optional
(
"-minAlternateDepth"
,
minAlternateDepth
)
+
optional
(
"-minSamplesPass"
,
minSamplesPass
)
+
conditional
(
filterRefCalls
,
"-filterRefCalls"
)
optional
(
"-
-
minSampleDepth"
,
minSampleDepth
)
+
optional
(
"-
-
minTotalDepth"
,
minTotalDepth
)
+
optional
(
"-
-
minAlternateDepth"
,
minAlternateDepth
)
+
optional
(
"-
-
minSamplesPass"
,
minSamplesPass
)
+
conditional
(
filterRefCalls
,
"-
-
filterRefCalls"
)
}
object
VcfFilter
extends
ToolCommand
{
...
...
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